Table 5 Three-way pathway comparison of hiPSCs/hESCs, hiPSCs/HFs, and hESCs/HFs on a public dataset.

From: Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs

Pathways

hiPSCs/hESCs (p-val /FDR)

hiPSCs/HFs (p-val/FDR)

hESCs/HFs (p-val/FDR)

KEGG: DNA replication

UP 0.096/0.245

UP 0.000/0.000

UP 0.000/0.000

KEGG: ECM-receptor interaction

UP 0.003/0.025

DOWN 0.000/0.000

DOWN 0.000/0.000

KEGG: arrhythmogenic right ventricular cardiomyopathy (ARVC)

UP 0.011/0.145

DOWN 0.051/0.060

DOWN 0.011/0.013

KEGG: focal adhesion*

UP 0.003/0.136

DOWN 0.000/0.000

DOWN 0.000/0.000

KEGG: regulation of actin cytoskeleton

UP 0.002/0.107

DOWN 0.000/0.000

DOWN 0.000/0.000

KEGG: epithelial cell signaling in helicobacter pylori infection

UP 0.083/0.247

DOWN 0.076/0.118

DOWN 0.017/0.021

REACTOME: cell surface interactions at the vascular wall

UP 0.002/0.185

DOWN 0.031/0.031

DOWN 0.004/0.006

REACTOME: integrin cell surface interactions

UP 0.003/0.123

DOWN 0.005/0.007

DOWN 0.004/0.005

REACTOME: glucose transport

DOWN 0.000/0.000

UP 0.000/0.000

UP 0.000/0.000

REACTOME: regulation of glucokinase by glucokinase regulatory protein

DOWN 0.000/0.000

UP 0.000/0.000

UP 0.000/0.000

REACTOME: transport of ribonucleoproteins into the host nucleus

DOWN 0.000/0.000

UP 0.000/0.000

UP 0.000/0.000

REACTOME: processing of capped intron-containing pre-mRNA

DOWN 0.000/0.000

UP 0.000/0.000

UP 0.000/0.000

REACTOME: NEP/NS2 interacts with the cellular export machinery

DOWN 0.027/0.030

UP 0.000/0.000

UP 0.000/0.000

KEGG: arginine and proline metabolism

DOWN 0.055/0.058

N/A 0.615 /0.684

UP 0.053/0.105

KEGG: fatty acid metabolism

DOWN 0.101/0.198

N/A 0.946/1.000

UP 0.025/0.078

KEGG: peroxisome

DOWN 0.000/0.001

N/A 0.589/0.623

N/A 0.388/0.553

REACTOME: TCA cycle and respiratory electron transport*

DOWN 0.000/0.042

N/A 0.999/1.000

N/A 0.327/0.442

REACTOME: respiratory electron transport ATP synthesis by chemiosmotic coupling and heat production by uncoupling proteins*

DOWN 0.086/0.224

N/A 0.728/0.778

N/A 0.558/0.641

REACTOME: pyruvate metabolism and citric acid (TCA) cycle

DOWN 0.000/0.005

N/A 0.998/1.000

N/A 0.539/0.639

  1. *Significant pathways found in both public dataset and our dataset; UP: up-regulation; DOWN: down-regulation; N/A: not applicable; hiPSCs: human induced pluripotent stem cells; hESCs: human embryonic stem cells; HF: human fibroblast; p-val: p-value; FDR: false discovery rate.
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